Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100606 |
| Name | oriT_pC23-89  |
| Organism | Escherichia coli |
| Sequence Completeness | intact |
| NCBI accession of oriT (coordinates [strand]) | NC_025180 (37737..37846 [+], 110 nt) |
| oriT length | 110 nt |
| IRs (inverted repeats) | IR1: 24..31, 35..42 (GTCGGGGC..GCCCTGAC) IR2: 49..65, 72..88 (GTAATTGTAATAGCGTC..GACGGTATTACAATTAC) |
| Location of nic site | 96..97 |
| Conserved sequence flanking the nic site |
CATCCTG|T |
| Note | predicted by the oriTfinder |
oriT sequence
Download Length: 110 nt
>oriT_pC23-89
TCACTTCAGGCTCCTTACGGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTCAGG
TCACTTCAGGCTCCTTACGGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTCAGG
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 678 | GenBank | YP_009071322 |
| Name | PutativerelaxaseofpC23-89 |
UniProt ID | A0A075MEJ3 |
| Length | 899 a.a. | PDB ID | |
| Note | putative relaxase | ||
Relaxase protein sequence
Download Length: 899 a.a. Molecular weight: 103883.32 Da Isoelectric Point: 7.3373
>YP_009071322.1 hypothetical protein (plasmid) [Escherichia coli]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIAQQAHYAKDNTDPVFHYILSWQAHESPRPEQIYDSVR
HTLKSLGLGEHQYVSAVHTDTDNLHVHVAVNRVHPVTGYLNCLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVNDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIAQQAHYAKDNTDPVFHYILSWQAHESPRPEQIYDSVR
HTLKSLGLGEHQYVSAVHTDTDNLHVHVAVNRVHPVTGYLNCLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVNDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | A0A075MEJ3 |
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 2944..32376
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| HTD68_RS00010 (D616_p154001) | 241..396 | - | 156 | WP_001302705 | hypothetical protein | - |
| HTD68_RS00515 | 1233..1655 | - | 423 | WP_162847923 | prepilin, shufflon protein A | - |
| HTD68_RS00025 (D616_p154004) | 1639..2793 | + | 1155 | WP_001139958 | site-specific integrase | - |
| HTD68_RS00030 (D616_p154005) | 2944..3768 | + | 825 | WP_001545755 | conjugal transfer protein TraE | traE |
| HTD68_RS00035 (D616_p154006) | 3854..5056 | + | 1203 | WP_000976353 | conjugal transfer protein TraF | - |
| HTD68_RS00040 (D616_p154007) | 5116..5700 | + | 585 | WP_000977522 | histidine phosphatase family protein | - |
| HTD68_RS00045 (D616_p154009) | 6095..6553 | + | 459 | WP_001079808 | IncI1-type conjugal transfer lipoprotein TraH | - |
| HTD68_RS00050 (D616_p154010) | 6550..7368 | + | 819 | WP_000646097 | IncI1-type conjugal transfer lipoprotein TraI | traI |
| HTD68_RS00055 (D616_p154011) | 7365..8513 | + | 1149 | WP_001024972 | plasmid transfer ATPase TraJ | virB11 |
| HTD68_RS00060 (D616_p154012) | 8510..8800 | + | 291 | WP_001372180 | hypothetical protein | traK |
| HTD68_RS00065 (D616_p154013) | 8815..9366 | + | 552 | WP_000014584 | phospholipase D family protein | - |
| HTD68_RS00070 (D616_p154014) | 9456..13223 | + | 3768 | WP_001141542 | LPD7 domain-containing protein | - |
| HTD68_RS00075 (D616_p154015) | 13241..13588 | + | 348 | WP_001055900 | conjugal transfer protein | traL |
| HTD68_RS00080 (D616_p154016) | 13585..14277 | + | 693 | WP_000138551 | DotI/IcmL family type IV secretion protein | traM |
| HTD68_RS00085 (D616_p154017) | 14288..15271 | + | 984 | WP_001191879 | IncI1-type conjugal transfer protein TraN | traN |
| HTD68_RS00090 (D616_p154018) | 15274..16563 | + | 1290 | WP_001272000 | conjugal transfer protein TraO | traO |
| HTD68_RS00095 (D616_p154019) | 16563..17267 | + | 705 | WP_000801919 | IncI1-type conjugal transfer protein TraP | traP |
| HTD68_RS00100 (D616_p154020) | 17267..17794 | + | 528 | WP_001055569 | conjugal transfer protein TraQ | traQ |
| HTD68_RS00105 (D616_p154021) | 17845..18249 | + | 405 | WP_000086959 | IncI1-type conjugal transfer protein TraR | traR |
| HTD68_RS00110 (D616_p154022) | 18313..18501 | + | 189 | WP_001277255 | putative conjugal transfer protein TraS | - |
| HTD68_RS00115 (D616_p154023) | 18485..19285 | + | 801 | WP_001164788 | IncI1-type conjugal transfer protein TraT | traT |
| HTD68_RS00120 (D616_p154024) | 19375..22419 | + | 3045 | WP_001024782 | IncI1-type conjugal transfer protein TraU | traU |
| HTD68_RS00125 (D616_p154026) | 22419..23033 | + | 615 | WP_000337399 | IncI1-type conjugal transfer protein TraV | traV |
| HTD68_RS00130 (D616_p154027) | 23000..24202 | + | 1203 | WP_001189160 | IncI1-type conjugal transfer protein TraW | traW |
| HTD68_RS00135 (D616_p154028) | 24231..24815 | + | 585 | WP_001037987 | IncI1-type conjugal transfer protein TraX | - |
| HTD68_RS00140 (D616_p154029) | 24912..27080 | + | 2169 | WP_000698357 | DotA/TraY family protein | traY |
| HTD68_RS00145 (D616_p154030) | 27130..27804 | + | 675 | WP_223866377 | plasmid IncI1-type surface exclusion protein ExcA | - |
| HTD68_RS00150 (D616_p154031) | 27876..28085 | - | 210 | WP_000062603 | HEAT repeat domain-containing protein | - |
| HTD68_RS00155 | 28369..28653 | + | 285 | WP_001707309 | hypothetical protein | - |
| HTD68_RS00525 | 28718..28813 | - | 96 | WP_001303310 | DinQ-like type I toxin DqlB | - |
| HTD68_RS00160 (D616_p154034) | 29312..29563 | + | 252 | WP_001291965 | hypothetical protein | - |
| HTD68_RS00165 (D616_p154035) | 29635..29787 | - | 153 | WP_001303307 | Hok/Gef family protein | - |
| HTD68_RS00170 (D616_p154036) | 30079..31287 | + | 1209 | WP_000121273 | IncI1-type conjugal transfer protein TrbA | trbA |
| HTD68_RS00175 (D616_p154037) | 31306..32376 | + | 1071 | WP_000151582 | IncI1-type conjugal transfer protein TrbB | trbB |
| HTD68_RS00180 (D616_p154038) | 32369..34660 | + | 2292 | WP_001289282 | F-type conjugative transfer protein TrbC | - |
Host bacterium
| ID | 1066 | GenBank | NC_025180 |
| Plasmid name | pC23-89 | Incompatibility group | IncI1 |
| Plasmid size | 89513 bp | Coordinate of oriT [Strand] | 37737..37846 [+] |
| Host baterium | Escherichia coli |
Cargo genes
| Drug resistance gene | blaTEM-52C |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |